$NetBSD$

--- Makefile.orig	2013-04-18 19:33:39.000000000 +0000
+++ Makefile
@@ -5,9 +5,9 @@
 SEQAN_DIR = SeqAn-1.1
 SEQAN_INC = -I $(SEQAN_DIR)
 INC = $(SEQAN_INC)
-CPP = g++
-CXX = $(CPP)
-CC = gcc
+# CPP = g++
+# CXX = $(CPP)
+# CC = gcc
 HEADERS = $(wildcard *.h)
 BOWTIE_MM = 1
 BOWTIE_SHARED_MEM = 1
@@ -47,6 +47,7 @@ ifneq (,$(findstring Linux,$(shell uname
     LINUX = 1
     EXTRA_FLAGS += -Wl,--hash-style=both
 endif
+LINUX = 1
 
 MM_DEF = 
 ifeq (1,$(BOWTIE_MM))
@@ -107,22 +108,22 @@ ifeq (1,$(MINGW))
 endif
 
 ifeq (1,$(LINUX))
-    ifeq (x86_64, $(shell uname -p))
+    ifeq (amd64, $(shell uname -p))
         BITS=64
     endif
 endif
 
 # Convert BITS=?? to a -m flag
 BITS_FLAG =
-ifeq (32,$(BITS))
-    BITS_FLAG = -m32
-endif
-ifeq (64,$(BITS))
-    BITS_FLAG = -m64
-endif
+#ifeq (32,$(BITS))
+    #BITS_FLAG = -m32
+#endif
+#ifeq (64,$(BITS))
+    #BITS_FLAG = -m64
+#endif
 
 DEBUG_FLAGS = -O0 -g3 $(BITS_FLAG)
-RELEASE_FLAGS = -O3 $(BITS_FLAG)
+RELEASE_FLAGS = # -O3 $(BITS_FLAG)
 NOASSERT_FLAGS = -DNDEBUG
 FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
 
@@ -179,7 +180,7 @@ DEFS=-fno-strict-aliasing \
      $(MM_DEF) \
      $(SHMEM_DEF)
 
-ALL_FLAGS = $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)
+ALL_FLAGS = $(EXTRA_FLAGS) $(CXXFLAGS)
 DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(ALL_FLAGS)\""
 RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(ALL_FLAGS)\""
 
